Government stressed it had to balance public safety and cost pressures on building owners. That stance was echoed by the Labour Party.
Local Government New Zealand president Lawrence Yule said some councils which were well-advanced in their assessments might question whether the new rules required a fast enough response to earthquake-related risks.
Between 15,000 and 25,000 buildings across the country were believed to be at risk of collapse in a moderate earthquake.
The Alpine fault, the most likely source of a catastrophic earthquake in New Zealand, had a 6 to 9 per cent chance of rupturing in the next 20 years. The Wellington Fault. which runs under the city's CBD, produced a large earthquake every 500 to 1000 years.
Mr Williamson said the rules had to reflect the risk posed by earthquakes.
Since 1843, 483 people have died in quakes - all but 43 in Napier in 1931 or Christchurch in 2011.
This compared to 37,000 deaths in road accidents. Auckland was considered a very low risk of a large earthquake - the closest faults moved every 13,000 to 43,000 years and the maximum ground acceleration was a tenth of that in Christchurch - but the minister said the city should not be complacent.
Financial incentives would be offered to those that strengthened their buildings, though the details would not be confirmed until later in the year.
The Property Council, which has been seeking tax breaks on strengthening work, said this concession by Government was a "huge breakthrough".
Some concern remained about whether the new policy provided sufficient protection for heritage buildings. The deadline of 2043 was only given to Category 1 buildings.
Of the 5657 buildings on the Historic Places Trust register, just 980 were classed as Category 1.
Labour deputy leader Grant Robertson said: "What we learned from Christchurch was that there were a lot of heritage buildings that people ... had a great attachment to, buildings that aren't covered by that classification. So we want to to see heritage building owners given time to ensure that we can protect our history."
Property Council chief Connal Townsend said strengthening heritage buildings was far more complex, "like open-heart surgery", and it was possible that some Category 2 buildings would not be able to be upgraded within the 20-year timeframe.
The requirement to upgrade earthquake-prone buildings to 34 per cent of the new building standard remained unchanged.
Mr Williamson noted that every percentage point increase led to $700 million of new costs for owners.